As it is known, changes in pH change the attractions between the groups in the side chains of the protein.

Acidification can, for example, cause protonation of the $\ce{COO-}$ end to $\ce{COOH},$ reducing interaction forces and provoking the unfold of the protein.

I would like to know if there is any software (or any resource) that, given the quaternary structure of a protein, allows you to visualize or obtain an analysis of how this structure will vary according to different pH values.

  • $\begingroup$ Knowing whether residues are solvent exposed and what other residues (groups) are nearby suffices to allow prediction of state of protonation. Beyond that the problem you outline becomes a bit hard to understand. How would you "give the quaternary structure of a protein"? What do you mean by that? $\endgroup$
    – Buck Thorn
    Commented Apr 27, 2021 at 9:09
  • $\begingroup$ The closest I can think of is protein-protein docking software. I would start with a web search for that. $\endgroup$
    – Buck Thorn
    Commented Apr 27, 2021 at 9:12
  • $\begingroup$ @BuckThorn, that´s exactly it. I want to perform a MD with the protein in the different states of protonation in order to quantify the affinity with different ligands. By the quaternary structure I mean the protein in it´s physiological active form, which is the structure used in the docking. How can I check whether the residues are solvent exposed? $\endgroup$
    – RoyBatty
    Commented Apr 27, 2021 at 16:47
  • 2
    $\begingroup$ Run the sim and look for solvent-protein contacts. Read the simulation software documentation to figure out how, or ask over at material modelling SE. $\endgroup$
    – Buck Thorn
    Commented Apr 27, 2021 at 19:22


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